水稻骨干亲本遗传效应的基础研究

顾红雅　汤述翥　李双成　陈浩东　梁婉琪

摘 要：水稻骨干亲本黄华占性状优良，育种谱系清晰，被选作该课题的主要研究对象之一。利用水稻的高通量测序结果，设计了一款超过5万位点的高密度SNP芯片，对黄华占谱系中的部分水稻品种进行了高通量基因分型，以发掘受到了人工选择的基因或位点；同时将此信息与重要农艺性状进行基于单倍体型的关联分析，鉴定到了几十个性状相关位点。比较桂朝2号、青六矮、丰矮占1号等高产品种和黄华占的穗型差异，发现这些品种的一次枝梗数目差异不大，而二次枝梗的数目有显著差异，说明二次枝梗数目可能是造成这些品种最终穗粒数差异的主要原因；通过比较分析发现，桂朝2号和黄华占中CKX2、Ghd7、DEP2以及IPA/SPL14等重要穗型控制基因的序列是一致的，而其他一些品种则发现有基因序列多态性存在。鉴定了矮仔占→桂朝2号→黄华占为主线的籼稻骨干亲本中sd1基因的等位性变异，发现5种变异类型；明确了桂朝2号及其衍生品种的均是利用低脚乌尖一类的sd1-d，而非矮仔占所带有的sd1；利用染色体片段代换系比较了骨干亲本扬稻6号（9311）sd1等位变异类型在籼、粳背景下的遗传效应。蜀恢527是由四川农业大学水稻研究所于2000年选育成功的强优势恢复系，具有一般配合力高、所配组合多、杂种优势强、千粒重较大等优点，被认为是杂交水稻的“第三代”代表恢复系。该研究广泛收集了527系谱亲本材料和目前在生产上广泛应用的衍生恢复系约30份，利用高密度水稻SNP芯片进行全基因组扫描确定骨干亲本基因组组成及区段确切来源；构建了527极其亲本和衍生材料的基因组高密度单倍型图谱，确定了骨干亲本527的关键基因组区域，初步检测了可能的重要农艺性状关联位点，为进一步确定关键基因组区段的重要控制（候选）基因、解析骨干亲本527的分子基础和遗传效应奠定了基础。同时，利用图位克隆方法，克隆了水稻结实率控制关键基因PTB1，证实了PTB1基因是控制水稻花粉管生长、調控水稻结实率的关键基因，首次解析了水稻结实率这一重要产量性状的分子机制，为进一步理解水稻花粉管生长和明确水稻结实率的相关调控通路提供了全新视点，并可能促进其在水稻高产稳产中的直接应用。同时，通过该基因在527系谱的分析，从结实率角度阐述了527及其衍生材料表现高结实率的分子基础。

关键词：黄华占 蜀恢527 骨干亲本 半矮秆基因 等位性变异 关键基因组区域 PTB1基因

Abstract：The backbone variety Huanhuazhan has many excellent agronomic traits， and most importantly is its clear breeding lineage. Therefore， Huanhuazhan and its derivatives have been selected as one of the key materials in this study. Based on the high-through put re-sequencing of rice genomes， a SNP chip with more than 50000 dots was designed. This chip was used for a high-through put genome-typing on the key rice varieties in Huanhuazhan lineage with the purpose of discovering genes or loci under human selection during rice cultivation. The association analysis of important agronomic traits and SNPs was performed， several dozen of associated loci were identified. Comparison of the panicle morphology of Huanghuazhan and its derivative varieties such as Guichao 2， Qingliuai， Fengaizhan 1 found that they had similar primary branching numbers， but different secondary branching numbers. It implies that the secondary branching number could be the major factor for the difference in final grain number/plant among the varieties. Gene sequence comparison found that some genes involving panicle morphology such as CKX2、Ghd7、DEP and IPA/SPL14 are quite similar in Huanghuazhan and Guichao 2， but different among other varieties. Analysis on the allelic variation of sd1 in the Aizizhan – Guichao 2 – Huanghuazhan lineage was performed， and five variation types were found among them. The gene sd1-d in Guichao 2 and its derivatives were from Deo-geo-woo-gen， not from Aizizhan （sd1）. The genetic effect of sd1 from 9311 （Yangdao 6） in both indica and japonica genomic background was tested using chromosomal segment substitution lines. Shuhui 527 was a very successful recover line， and it has been widely used a breeding material for its strong heterosis and heavy thousand-grain weight. More than 30 recover lines and other Shuhui 527 derivative varieties or lines were used for a genomic scanning to identify the fragments inherited from Shuhui 527. A high density hap-map of Shuhui 527 and its parental and derivative lines was constructed， and some key backbone fragments were identified. GWAS analysis found several sites which was associated with the most important yield-related traits. A key gene controlling seed-set， PTB1， was cloned using map-based cloning method. This gene is involved in controlling pollen tube. The variation pattern of PTB1 in Shuhui 527 and its parental and derivative lines provided a molecular basis for the high seed-set of Shuhui 527 and its derivatives.

Key Words：Huanghuazhan； Shuhui 527； Backbone varieties； Semi-dwarf gene； Allelic variation； Key genomic region； PTB1

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